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//
// classifysharedcommand.h
// Mothur
//
// Created by Abu Zaher Md. Faridee on 8/13/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#ifndef __Mothur__classifyrfsharedcommand__
#define __Mothur__classifyrfsharedcommand__
#include "command.hpp"
#include "inputdata.h"
class ClassifyRFSharedCommand : public Command {
public:
ClassifyRFSharedCommand();
ClassifyRFSharedCommand(string);
~ClassifyRFSharedCommand() {};
vector<string> setParameters();
string getCommandName() { return "classify.rf"; }
string getCommandCategory() { return "OTU-Based Approaches"; }
string getHelpString();
string getOutputPattern(string);
string getCitation() { return "http://www.mothur.org/wiki/Classify.rf\n"; }
string getDescription() { return "implements the random forest machine learning algorithm to identify OTUs that can be used to differentiate between various groups of samples"; }
int execute();
void help() { m->mothurOut(getHelpString()); }
private:
bool abort;
string outputDir;
vector<string> outputNames, Groups;
string sharedfile, designfile;
set<string> labels;
bool allLines;
int processors;
bool useTiming;
GroupMap designMap;
int numDecisionTrees;
string treeSplitCriterion, optimumFeatureSubsetSelectionCriteria;
bool doPruning, discardHighErrorTrees;
double pruneAggressiveness, highErrorTreeDiscardThreshold, featureStandardDeviationThreshold;
void processSharedAndDesignData(vector<SharedRAbundVector*> lookup);
};
#endif /* defined(__Mothur__classifyrfsharedcommand__) */
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